kim-tools 0.2.0b0__py3-none-any.whl

kim_tools/symmetry_util/core.py

@@ -0,0 +1,552 @@
+"""
+Crystal Symmetry utilities and data that are (mostly) independent of AFLOW
+"""
+
+import json
+import logging
+import os
+from itertools import product
+from math import ceil
+from typing import Dict, List, Union
+
+import numpy as np
+from ase import Atoms
+from ase.cell import Cell
+from ase.geometry import get_duplicate_atoms
+from numpy.typing import ArrayLike
+from sympy import Matrix, cos, matrix2numpy, sin, sqrt, symbols
+
+logger = logging.getLogger(__name__)
+logging.basicConfig(filename="kim-tools.log", level=logging.INFO, force=True)
+
+__all__ = [
+    "BRAVAIS_LATTICES",
+    "FORMAL_BRAVAIS_LATTICES",
+    "CENTERING_DIVISORS",
+    "C_CENTERED_ORTHORHOMBIC_GROUPS",
+    "A_CENTERED_ORTHORHOMBIC_GROUPS",
+    "IncorrectCrystallographyException",
+    "IncorrectNumAtomsException",
+    "are_in_same_wyckoff_set",
+    "space_group_numbers_are_enantiomorphic",
+    "cartesian_to_fractional_itc_rotation_from_ase_cell",
+    "cartesian_rotation_is_in_point_group",
+    "get_cell_from_poscar",
+    "get_wyck_pos_xform_under_normalizer",
+    "get_bravais_lattice_from_space_group",
+    "get_formal_bravais_lattice_from_space_group",
+    "get_primitive_wyckoff_multiplicity",
+    "get_symbolic_cell_from_formal_bravais_lattice",
+    "get_change_of_basis_matrix_to_conventional_cell_from_formal_bravais_lattice",
+    "change_of_basis_atoms",
+    "get_possible_primitive_shifts",
+    "get_primitive_genpos_ops",
+]
+
+C_CENTERED_ORTHORHOMBIC_GROUPS = (20, 21, 35, 36, 37, 63, 64, 65, 66, 67, 68)
+A_CENTERED_ORTHORHOMBIC_GROUPS = (38, 39, 40, 41)
+BRAVAIS_LATTICES = [
+    "aP",
+    "mP",
+    "mC",
+    "oP",
+    "oC",
+    "oI",
+    "oF",
+    "tP",
+    "tI",
+    "hP",
+    "hR",
+    "cP",
+    "cF",
+    "cI",
+]
+FORMAL_BRAVAIS_LATTICES = BRAVAIS_LATTICES + ["oA"]
+CENTERING_DIVISORS = {
+    "P": 1,
+    "C": 2,
+    "A": 2,
+    "I": 2,
+    "F": 4,
+    "R": 3,
+}
+DATA_DIR = os.path.join(os.path.dirname(os.path.realpath(__file__)), "data")
+
+
+class IncorrectCrystallographyException(Exception):
+    """
+    Raised when incorrect data is provided, e.g. nonexistent Bravais lattice etc.
+    """
+
+
+class IncorrectNumAtomsException(Exception):
+    """
+    Raised when the a disagreement in the number of atoms is found.
+    """
+
+
+def _check_space_group(sgnum: Union[int, str]):
+    try:
+        assert 1 <= int(sgnum) <= 230
+    except Exception:
+        raise IncorrectCrystallographyException(
+            f"Got a space group number {sgnum} that is non-numeric or not between 1 "
+            "and 230 inclusive"
+        )
+
+
+def cartesian_to_fractional_itc_rotation_from_ase_cell(
+    cart_rot: ArrayLike, cell: ArrayLike
+) -> ArrayLike:
+    """
+    Convert Cartesian to fractional rotation. Read the arguments and returns carefully,
+    as there is some unfortunate mixing of row and columns because of the different
+    conventions of the ITC and ASE and other simulation packages
+
+    Args:
+        cart_rot:
+            Cartesian rotation. It is assumed that this is for left-multiplying column
+            vectors, although in cases where we don't care if we're working with the
+            rotation or its inverse (e.g. when checking whether or not it's in the
+            point group), this doesn't matter due to orthogonality
+        cell:
+            The cell of the crystal, with each row being a cartesian vector
+            representing a lattice vector. This is consistent with most simulation
+            packages, but transposed from the ITC
+
+    Returns:
+        The fractional rotation in ITC convention, i.e. for left-multiplying column
+        vectors. Here the distinction with a matrix's transpose DOES matter, because
+        the fractional coordinate system is not orthonormal.
+    """
+
+    cell_arr = np.asarray(cell)
+    cart_rot_arr = np.asarray(cart_rot)
+
+    if not ((cell_arr.shape == (3, 3)) and (cart_rot_arr.shape == (3, 3))):
+        raise IncorrectCrystallographyException(
+            "Either the rotation matrix or the cell provided were not 3x3 matrices"
+        )
+
+    return np.transpose(cell_arr @ cart_rot_arr @ np.linalg.inv(cell_arr))
+
+
+def cartesian_rotation_is_in_point_group(
+    cart_rot: ArrayLike, sgnum: Union[int, str], cell: ArrayLike
+) -> bool:
+    """
+    Check that a Cartesian rotation is in the point group of a crystal given by its
+    space group number and primitive cell
+
+    Args:
+        cart_rot:
+            Cartesian rotation
+        sgnum:
+            space group number
+        cell:
+            The *primitive* cell of the crystal as defined in
+            http://doi.org/10.1016/j.commatsci.2017.01.017, with each row being a
+            cartesian vector representing a lattice vector. This is
+            consistent with most simulation packages, but transposed from the ITC
+    """
+    # we don't care about properly transposing (i.e. worrying whether it's operating on
+    # row or column vectors) the input cart_rot because that one is orthogonal, and
+    # both it and its inverse must be in the point group
+    frac_rot = cartesian_to_fractional_itc_rotation_from_ase_cell(cart_rot, cell)
+
+    space_group_ops = get_primitive_genpos_ops(sgnum)
+
+    for op in space_group_ops:
+        if np.allclose(frac_rot, op["W"], atol=1e-4):
+            logger.info("Found matching rotation")
+            return True
+
+    logger.info("No matching rotation found")
+    return False
+
+
+def get_cell_from_poscar(poscar: os.PathLike) -> ArrayLike:
+    """
+    Extract the unit cell from a POSCAR file, including the specified scaling
+    """
+    with open(poscar) as f:
+        poscar_lines = f.read().splitlines()
+
+    scaling = float(poscar_lines[1])
+    cell = np.asarray(
+        [[float(num) for num in line.split()] for line in poscar_lines[2:5]]
+    )
+
+    if scaling < 0:
+        desired_volume = -scaling
+        unscaled_volume = Cell(cell).volume
+        scaling = (desired_volume / unscaled_volume) ** (1 / 3)
+
+    return cell * scaling
+
+
+def are_in_same_wyckoff_set(letter_1: str, letter_2: str, sgnum: Union[str, int]):
+    """
+    Given two Wyckoff letters and a space group number, return whether or not they are
+    in the same Wyckoff set, meaning that their orbits are related by an operation in
+    the normalizer of the space group
+    """
+    _check_space_group(sgnum)
+    with open(os.path.join(DATA_DIR, "wyckoff_sets.json")) as f:
+        wyckoff_sets = json.load(f)
+    for wyckoff_set in wyckoff_sets[str(sgnum)]:
+        if letter_1 in wyckoff_set:
+            if letter_2 in wyckoff_set:
+                return True
+            else:
+                return False
+
+
+def space_group_numbers_are_enantiomorphic(sg_1: int, sg_2: int) -> bool:
+    """
+    Return whether or not two spacegroups (specified by number) are enantiomorphs of
+    each other
+    """
+    _check_space_group(sg_1)
+    _check_space_group(sg_2)
+    if sg_1 == sg_2:
+        return True
+    else:
+        enantiomorph_conversion = {
+            78: 76,
+            95: 91,
+            96: 92,
+            145: 144,
+            153: 151,
+            154: 152,
+            170: 169,
+            172: 171,
+            179: 178,
+            181: 180,
+            213: 212,
+        }
+        enantiomorph_conversion_2 = {v: k for k, v in enantiomorph_conversion.items()}
+        enantiomorph_conversion.update(enantiomorph_conversion_2)
+        if enantiomorph_conversion[sg_1] == sg_2:
+            return True
+        else:
+            return False
+
+
+def get_wyck_pos_xform_under_normalizer(sgnum: Union[int, str]) -> List[List[str]]:
+    """
+    Get the "Transformed WP" column of the tables at the bottom of the page for each
+    space group from https://cryst.ehu.es/cryst/get_set.html
+    """
+    _check_space_group(sgnum)
+    with open(os.path.join(DATA_DIR, "wyck_pos_xform_under_normalizer.json")) as f:
+        wyck_pos_xform_under_normalizer = json.load(f)
+    return wyck_pos_xform_under_normalizer[str(sgnum)]
+
+
+def get_bravais_lattice_from_space_group(sgnum: Union[int, str]):
+    """
+    Get the symbol (e.g. 'cF') of one of the 14 Bravais lattices from the space group
+    number
+    """
+    _check_space_group(sgnum)
+    with open(
+        os.path.join(DATA_DIR, "space_groups_for_each_bravais_lattice.json")
+    ) as f:
+        space_groups_for_each_bravais_lattice = json.load(f)
+    for bravais_lattice in space_groups_for_each_bravais_lattice:
+        if int(sgnum) in space_groups_for_each_bravais_lattice[bravais_lattice]:
+            return bravais_lattice
+    raise RuntimeError(
+        f"Failed to find space group number f{sgnum} in table of lattice symbols"
+    )
+
+
+def get_formal_bravais_lattice_from_space_group(sgnum: Union[int, str]):
+    """
+    Same as :func:`get_bravais_lattice_from_space_group` except distinguish between "oA"
+    and "oC"
+    """
+    bravais_lattice = get_bravais_lattice_from_space_group(sgnum)
+    if bravais_lattice == "oC":
+        if int(sgnum) in A_CENTERED_ORTHORHOMBIC_GROUPS:
+            return "oA"
+        else:
+            assert int(sgnum) in C_CENTERED_ORTHORHOMBIC_GROUPS
+    return bravais_lattice
+
+
+def get_primitive_wyckoff_multiplicity(sgnum: Union[int, str], wyckoff: str) -> int:
+    """
+    Get the multiplicity of a given Wyckoff letter for a primitive cell of the crystal
+    """
+    _check_space_group(sgnum)
+    centering_divisor = CENTERING_DIVISORS[
+        get_bravais_lattice_from_space_group(sgnum)[1]
+    ]
+    with open(os.path.join(DATA_DIR, "wyckoff_multiplicities.json")) as f:
+        wyckoff_multiplicities = json.load(f)
+    multiplicity_per_primitive_cell = (
+        wyckoff_multiplicities[str(sgnum)][wyckoff] / centering_divisor
+    )
+    # check that multiplicity is an integer
+    assert np.isclose(
+        multiplicity_per_primitive_cell, round(multiplicity_per_primitive_cell)
+    )
+    return round(multiplicity_per_primitive_cell)
+
+
+def get_symbolic_cell_from_formal_bravais_lattice(
+    formal_bravais_lattice: str,
+) -> Matrix:
+    """
+    Get the symbolic primitive unit cell as defined in
+    http://doi.org/10.1016/j.commatsci.2017.01.017 in terms of the appropriate
+    (possibly trivial) subset of the parameters a, b, c, alpha, beta, gamma
+
+    Args:
+        formal_bravais_lattice:
+            The symbol for the Bravais lattice, e.g "oA". Specifically, "oA" is
+            distinguished from "oC", meaning there are 15 possibilities, not just the
+            14 Bravais lattices.
+
+    Returns:
+        Symbolic 3x3 matrix with the rows being cell vectors. This is in agreement with
+        most simulation software, but the transpose of how the ITA defines cell vectors.
+
+    Raises:
+        IncorrectCrystallographyException:
+            If a nonexistent Bravais lattice is provided
+    """
+    if formal_bravais_lattice not in FORMAL_BRAVAIS_LATTICES:
+        raise IncorrectCrystallographyException(
+            f"The provided Bravais lattice type {formal_bravais_lattice} "
+            "does not exist."
+        )
+
+    a, b, c, alpha, beta, gamma = symbols("a b c alpha beta gamma")
+
+    if formal_bravais_lattice == "aP":
+        c_x = c * cos(beta)
+        c_y = c * (cos(alpha) - cos(beta) * cos(gamma)) / sin(gamma)
+        c_z = sqrt(c**2 - c_x**2 - c_y**2)
+        return Matrix([[a, 0, 0], [0, b * cos(gamma), b * sin(gamma)], [c_x, c_y, c_z]])
+    elif formal_bravais_lattice == "mP":
+        return Matrix([[a, 0, 0], [0, b, 0], [c * cos(beta), 0, c * sin(beta)]])
+    elif formal_bravais_lattice == "mC":
+        return Matrix(
+            [[a / 2, -b / 2, 0], [a / 2, b / 2, 0], [c * cos(beta), 0, c * sin(beta)]]
+        )
+    elif formal_bravais_lattice == "oP":
+        return Matrix([[a, 0, 0], [0, b, 0], [0, 0, c]])
+    elif formal_bravais_lattice == "oC":
+        return Matrix([[a / 2, -b / 2, 0], [a / 2, b / 2, 0], [0, 0, c]])
+    elif formal_bravais_lattice == "oA":
+        return Matrix([[a, 0, 0], [0, b / 2, -c / 2], [0, b / 2, c / 2]])
+    elif formal_bravais_lattice == "oI":
+        return Matrix(
+            [[-a / 2, b / 2, c / 2], [a / 2, -b / 2, c / 2], [a / 2, b / 2, -c / 2]]
+        )
+    elif formal_bravais_lattice == "oF":
+        return Matrix([[0, b / 2, c / 2], [a / 2, 0, c / 2], [a / 2, b / 2, 0]])
+    elif formal_bravais_lattice == "tP":
+        return Matrix([[a, 0, 0], [0, a, 0], [0, 0, c]])
+    elif formal_bravais_lattice == "tI":
+        return Matrix(
+            [[-a / 2, a / 2, c / 2], [a / 2, -a / 2, c / 2], [a / 2, a / 2, -c / 2]]
+        )
+    elif formal_bravais_lattice == "hP":
+        return Matrix(
+            [[a / 2, -sqrt(3) * a / 2, 0], [a / 2, sqrt(3) * a / 2, 0], [0, 0, c]]
+        )
+    elif formal_bravais_lattice == "hR":
+        return Matrix(
+            [
+                [a / 2, -a / (2 * sqrt(3)), c / 3],
+                [0, a / sqrt(3), c / 3],
+                [-a / 2, -a / (2 * sqrt(3)), c / 3],
+            ]
+        )
+    elif formal_bravais_lattice == "cP":
+        return Matrix(
+            [
+                [a, 0, 0],
+                [0, a, 0],
+                [0, 0, a],
+            ]
+        )
+    elif formal_bravais_lattice == "cI":
+        return Matrix(
+            [[-a / 2, a / 2, a / 2], [a / 2, -a / 2, a / 2], [a / 2, a / 2, -a / 2]]
+        )
+    elif formal_bravais_lattice == "cF":
+        return Matrix([[0, a / 2, a / 2], [a / 2, 0, a / 2], [a / 2, a / 2, 0]])
+    else:
+        assert False
+
+
+def get_change_of_basis_matrix_to_conventional_cell_from_formal_bravais_lattice(
+    formal_bravais_lattice: str,
+) -> ArrayLike:
+    """
+    Get a change of basis matrix **P** as defined in ITA 1.5.1.2, with "old basis"
+    being the primitive cell of the provided Bravais lattice, and the "new basis" being
+    the conventional cell, i.e. the cell of the primitive lattice of the same crystal
+    family. E.g. if ``formal_bravais_lattice="oA"``, then "old basis" is oA, and
+    "new basis" is oP. The cell choices are defined in
+    http://doi.org/10.1016/j.commatsci.2017.01.017,
+    including distinguishing between oA and oC.
+
+    The matrices are given in ITC convention, meaning that they expect to operate on
+    column vectors, i.e. The bases are related by the following, where the primed
+    symbols indicate the new basis:
+
+    Relationship between basis vectors:
+    (**a**', **b**', **c**') = (**a**, **b**, **c**) **P**
+
+    Relationship between fractional coordinates in each basis: **x** = **P** **x**'
+
+    For operating on row vectors, as is often given in simulation software, make sure
+    to transpose these relationships appropriately.
+
+    Args:
+        formal_bravais_lattice:
+            The symbol for the Bravais lattice, e.g "oA". Specifically, "oA" is
+            distinguished from "oC", meaning there are 15 possibilities, not just the
+            14 Bravais lattices.
+
+    Returns:
+        Integral 3x3 matrix representing the change of basis
+
+    Raises:
+        IncorrectCrystallographyException:
+            If a nonexistent Bravais lattice is provided
+    """
+    if formal_bravais_lattice not in FORMAL_BRAVAIS_LATTICES:
+        raise IncorrectCrystallographyException(
+            f"The provided Bravais lattice type {formal_bravais_lattice} "
+            "does not exist."
+        )
+
+    if formal_bravais_lattice[1] == "P":  # Already primitive
+        return np.eye(3)
+
+    corresponding_primitive_lattice = formal_bravais_lattice[0] + "P"
+
+    old_basis = get_symbolic_cell_from_formal_bravais_lattice(
+        formal_bravais_lattice
+    ).transpose()
+    new_basis = get_symbolic_cell_from_formal_bravais_lattice(
+        corresponding_primitive_lattice
+    ).transpose()
+
+    change_of_basis_matrix = matrix2numpy((old_basis**-1) @ new_basis, dtype=float)
+
+    # matrices should be integral
+    assert np.allclose(np.round(change_of_basis_matrix), change_of_basis_matrix)
+
+    return np.round(change_of_basis_matrix)
+
+
+def change_of_basis_atoms(atoms: Atoms, change_of_basis: ArrayLike) -> Atoms:
+    """
+    Perform an arbitrary basis change on an ``Atoms`` object, duplicating or cropping
+    atoms as needed. A basic check is made that the determinant of ``change_of_basis``
+    is compatible with the number of atoms, but this is far from fully determining
+    that ``change_of_basis`` is appropriate for the particuar crystal described by
+    ``atoms``, which is up to the user.
+
+    NOTE: This requires ASE >= 3.25 to delete atoms that are close across PBCs
+
+    Args:
+        atoms:
+            The object to transform
+        change_of_basis:
+            A change of basis matrix **P** as defined in ITA 1.5.1.2, with ``atoms``
+            corresponding to the "old basis" and the returned ``Atoms`` object being
+            in the "new basis".
+
+            This matrix should be given in ITC convention, meaning that it expects to
+            operate on column vectors, i.e. The bases are related by the following,
+            where the primed symbols indicate the new basis:
+
+            Relationship between basis vectors:
+            (**a**', **b**', **c**') = (**a**, **b**, **c**) **P**
+
+            Relationship between fractional coordinates in each basis:
+            **x** = **P** **x**'
+
+    Returns:
+        The transformed ``Atoms`` object, containing the original number of
+        atoms mutiplied by the determinant of the change of basis.
+    """
+    old_cell_column = np.transpose(atoms.cell)
+    new_cell_column = old_cell_column @ change_of_basis
+    new_cell = np.transpose(new_cell_column)
+
+    # There are surely better ways to do this, but the simplest way I can think of
+    # is simply to use ``Atoms.repeat()`` to create a supercell big enough to encase
+    # the ``new_cell``, then wrap the atoms back into ``new_cell`` and delete dupes
+    repeat = []
+    for old_cell_vector in atoms.cell:
+        this_repeat = 0
+        old_cell_vector_norm = np.linalg.norm(old_cell_vector)
+        old_cell_vector_unit = old_cell_vector / old_cell_vector_norm
+        # We need to repeat the old vector enough times that it is big enough
+        # to cover all possible combinations of projected new vectors
+        projections = [
+            np.dot(new_cell_vector, old_cell_vector_unit)
+            for new_cell_vector in new_cell
+        ]
+        absmax_projected_sum = 0
+        for coeffs in product((-1, 1), repeat=3):
+            projected_sum = np.dot(coeffs, projections)
+            absmax_projected_sum = max(absmax_projected_sum, abs(projected_sum))
+        absmax_projected_sum += 0.1  # pad it a little bit
+        this_repeat = ceil(absmax_projected_sum / old_cell_vector_norm)
+        repeat.append(this_repeat)
+
+    new_atoms = atoms.repeat(repeat)
+    new_atoms.set_cell(new_cell)
+    new_atoms.wrap()
+    get_duplicate_atoms(new_atoms, delete=True)
+
+    volume_change = np.linalg.det(change_of_basis)
+    if not np.isclose(len(atoms) * volume_change, len(new_atoms)):
+        raise IncorrectNumAtomsException(
+            f"The change in the number of atoms from {len(atoms)} to {len(new_atoms)} "
+            f"disagrees with the fractional change in cell volume {volume_change}"
+        )
+
+    return new_atoms
+
+
+def get_possible_primitive_shifts(sgnum: Union[int, str]) -> List[List[float]]:
+    """
+    Get all unique translation parts of operations in the space group's normalizer that
+    don't leave the primitive cell. Given in the primitive basis as defined in
+    http://doi.org/10.1016/j.commatsci.2017.01.017
+
+    Args:
+        sgnum: space group number
+    """
+    _check_space_group(sgnum)
+    with open(os.path.join(DATA_DIR, "possible_primitive_shifts.json")) as f:
+        return json.load(f)[str(sgnum)]
+
+
+def get_primitive_genpos_ops(sgnum: Union[int, str]) -> List[Dict]:
+    """
+    Get the matrices and columns of the space group operations in the primitive setting
+    as defined in http://doi.org/10.1016/j.commatsci.2017.01.017
+
+    Args:
+        sgnum: space group number
+
+    Returns:
+        List of dictionaries, with each dictionary containing a matrix 'W' and
+        translation 'w' as generally defined in the ITA, but in the primitive setting.
+    """
+    _check_space_group(sgnum)
+    with open(os.path.join(DATA_DIR, "primitive_GENPOS_ops.json")) as f:
+        return np.asarray(json.load(f)[str(sgnum)])

kim_tools/symmetry_util/data/possible_primitive_shifts.json

@@ -0,0 +1 @@
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